He held an amateur record of 3-0 before turning professional at the age of 17. He lost his professional debut against Sammy Say but defeated him in his next bout to move to 1-1.

At the event, IFC: Road to Global Domination, he lost to Josh Neer but rebounded with a win over Jeff Lindsay. Waldburger defeated UFC veteran Pete Spratt via triangle choke submission in the second round. Spratt demanded a rematch and got one defeating Waldburger via knockout. He lost another fight before winning three straight. His early accomplishments include winning the Shark Fights Welterweight Championship belt in May 2009 and then defending it in September 2009.

Waldburger was expected to face Daniel Roberts on September 17, 2011 at UFC Fight Night 25.[6] However, Roberts was forced out of the bout with an injury and replaced by promotional newcomer Mike Stumpf.[7] Waldburger defeated Stumpf via first round triangle choke submission earning Submission of the Night honors.

Waldburger next faced Jake Hecht on March 3, 2012 at UFC on FX 2.[8] He won the fight via submission in the first round.

Waldburger faced Adlan Amagov on October 19, 2013 at UFC 166.[13] He lost the fight by knockout in the first round.

Waldburger faced Mike Pyle on February 22, 2014 at UFC 170.[14] He lost the fight via TKO in the third round.

Waldburger was expected to face Wendell Oliveira on February 22, 2015 at UFC Fight Night 61.[15] However, the fight was cancelled on the day of the weigh ins, as Waldburger passed out while cutting weight. Both fighters were paid their show money.[16]